Similarity maps for atom-pairs (AP) fingerprint. Similarity map of molecule 2 (middle) and molecule 3 (right) using AP. The reference compound is molecule 1 (left). Color scheme: removing bits decreases similarity (i.e. positive difference) (green), no change in similarity (gray), removing bits increases similarity (i.e. negative difference) (pink). The default maximum path length of 30 was used for AP.